Control of Gene Expression Flashcards
Describe seven levels at which gene expression can be regulated in eukaryotes.
- When and how often a given gene is transcribed
- How an mRNA transcript is spliced/processed
- Which mRNAs are exported from nucleus
- Stability of mRNA
- What proteins are translated (whether to translate transcript or not)
- How rapidly protein is turned over (degraded)
* Use ubiquitin to go to proteasome - The activity of proteins (post translational modifications, e.g., phosphorylation)
How do regulatory regions work to control gene expression in eukaryotes? How is this achieved?
What is a major way gene expression is controlled in prokaryotes?
Operons
(1) What are microRNAs? (2) How do they work?
(1) MicroRNAs (miRNAs) - tiny RNAs that control gene expression by base-pairing with specific mRNAs
(2)
(1) What is pluripotency? (2) How do stem cells maintain pluripotency?
(1) Pluripotency - undifferentiated cells are capable of giving rise to all specialized cell types
With respect to the lac operon→ What is the state of cAMP, CAP, the operator, the lac repressor and RNA polymerase under the following conditions? Also, under what condition is the operon functional?
- Nothing = operon off (CAP and Lac repressor bound)
- Glucose + lactose = operon off (Nothing bound)
- Only lactose = operon on (CAP bound)
- Only glucose = operon off (Lac repressor bound)
Compare housekeeping proteins and specialized proteins. Give some examples of each.
Housekeeping proteins - proteins common to all cells
Ex: DNA/RNA polymerase, enzymes involved in metabolism, DNA repair enzymes, cytoskeletal proteins
Specialized proteins - proteins responsible for a cell’s distinctive functions (limited to certain cell types)
Ex: regulatory enzymes/factors (e.g., gene-specific transcription factors), cell specific proteins (e.g, hemoglobin in RBCs, keratin in skin cells)
What are transcription regulators?
Proteins that bind to regulatory DNA sequences
What is the importance of dimerization?
Increases:
1. Area of contact with DNA
2. Potential strength and specificity of protein-DNA interaction
What is nanog? (1) What type of transcription factor is it and (2) what is its role?
(1) Gene specific transcription factor
(2) Helps stem cells maintain pluripotency
In bacteria, all amino acids are _________.
Nonessential
What conditions turn the Trp operon on and off?
When Trp level are low = open is transcribed
When Trp levels are high = operon is shut down
Describe the Trp repressor.
Uses tryptophan to activate repressor (Repressor will not engage if tryptophan is not present)
Describe the characteristics of operons.
- Encode polycistronic mRNA
- Specific to bacteria
- Allow for coordinate expression of genes involved in a common function
- Are under control of cis-acting sequnece (tied to gene) called operator that binds to negative regulators (repressors)
Compare cis-acting and trans-acting sequences.
- Cis-acting sequences - tied to gene
- Trans-acting sequences - protein that interacts with regulatory sequence (e.g., repressor)
What is the LacZ gene? What enzyme does it encode for and what is the function of that enzyme?
Encodes beta-galactosidase (breaks down lactose into galactose and glucose)
What are enhancers?
DNA sites where eukaryotic gene activators bind
What is the function of the mediator protein?
facilitate communication between transcription factors and RNA polymerase to regulate gene expression
What does polycistronic mean?
mRNAs encode several different proteins on same molecule
What would happen in mutant cells that prevent loops from forming?
Enhancers affecting multiple genes (cross talk)
What is the difference between general and gene-specific transcription factors?
General transcription factors:
* Set up at promoter
* Required for RNA Pol to dock
Gene-specific transcription factors:
* Stabilize complex
* Bind enhancers
Transcription regulators recruit:
Histone acetyl transferases (add acetyl groups to lysine of histone tails) - serve as binding sites for transcription activators and also neutralize (+) on histone
Chromatin-remodeling complexes - help open chromatin and help expose promoters to general transcription factors
Explain the Eve gene.
Early fruit fly development: segmented patterning (sets domains)
7 strips - even skipped gene
Artificial gene:
- TATA box
- Isolate regulatory region (stripe 2 regulatory segment)
- Enhancers placed to see which enhancer does what
- Exgal (Turns blue when cleaved)
- Stripe 2 regulatory DNA segment
Many enhancers
–> 4 different proteins
–> 2 activators
–> 2 repressors
–> Regulatory regions can be broken up with multiple enhancers
–> Regions have different combinations of activators/repressors
What is combinatorial control?
Process by which groups of transcription regulators work together to determine expression of a single gene
What are examples of combinatorial control?
Muscle cells - upregulate muscle specific forms of actin, myosin and receptors proteins/ion channels involved in muscle contractions
Endocrine cells - upregulate specialized components of secretory pathway
Nerve cells - upregulate proteins involved in propagating an action potential
What are induced pluripotent stem (iPS) cells?
Cells induced by artificial expression of specific transcription regulators to look and behave like pluripotent embryonic stem cells derived from embryos
Describe Klf, Oct4, Sox2 genes
- Each can reinforce themselves (activate their own promoters)
- Genes involved in maintaining stem cell nature
- Removal causes differentiation of cells
Why are stem cells important?
They can potentially differentiate into a multitude of different tissues
Give two examples of the influence of transcriptional regulators on reprogramming cells in culture.
- Liver cells -> artificially express nerve-specific transcription factors -> nerve cells
- Fibroblast cells derived from skin -> artificially express MyoD transcription factor -> form muscle cells
(1) What is UTR? (2) Does it get translated? (3) What is a 5’ untranslated region and a 3’ untranslated region?
(1) UTR - untranslated region
(2) No
(3)
- 5’ UTR =
- 3’ UTR = region of RNA that extends from stop codon to start of poly-A tail
What type of genes encode mRNAs that are regulated this way?
Heat shock proteins (Chaperone proteins)
What are regulatory RNAs? What are some examples?
noncoding RNAs that play a role in regulating gene expression.
Examples:
* microRNAs
* small interfering RNAs
* CRISPR RNAs
* long noncoding RNAs
microRNAs are expressed by which RNA polymerase?
RNA Pol II
Are microRNAs found in prokaryotes?
No
What are the two outcomes of mRNA?
- Perfect match = mRNA is degraded by nuclease within RISC
- Not perfect match but significant = prevent translation; mRNA is transferred to an are of cytoplasm where other nucleases destroy it
What is a dicer?
enzyme that cleaves double stranded RNA (dices up precursor microRNA)
Give an example of how cell differentiation can exit within organs/tissue types.
Pancreas:
- alpha cells = produce glucagon
- beta cells = produce insulin
Which is the most critical level of control for majority of genes?
Transcriptional control (level 1)
Transcription regulators interact with specific DNA sequences in what part of DNA?
Major groove
Explain how tryptophan affects the trp repressor.
Excess tryptophan - wedges into repressor so it can bind to operator
Low tryptophan - repressor cannot lock into operator (transcription is turned on)
What is the preferred sugar for bacteria?
Glucose
What is lactose made up of?
- Galactose
- Glucose
What inhibits adenylyl cyclase?
Glucose
What inhibits Lac repressor?
Lactose
What enzyme generates cAMP? What activator does cAMP activate?
(1) Adenylyl cyclase
(2) CAP
What would promote transcriptional repression in eukaryotes?
Histone deacetyl transferases - remove acetyl groups
